scholarly journals The dna barcoding data and genetic distance of leaf beetles (Coleoptera, Chrysomelidae) in Vietnam

2020 ◽  
Vol 42 (4) ◽  
Author(s):  
Nguyen Thi Dinh
Keyword(s):  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Coi Gene ◽  
Biodiversity Assessment ◽  
Leaf Beetles ◽  
The World ◽  
Living Organisms

DNA barcoding is a useful tool in identifying species, biodiversity assessment, and revealing phylogenetic relationships of living organisms in the world. However, the DNA barcode data for leaf beetles in Vietnam is lacking. In this study, sixteen DNA sequences of 658 bp of COI gene from nine species (five genera; three subfamilies) of Chrysomelidae in Vietnam were (obtained). Intra- and inter-specific diversities, and phylogenetic relationships of these species were analyzed. 

scholarly journals DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY

2020 ◽  
Vol 26 (2) ◽  
pp. 97
Author(s):  
Melta R. Fahmi ◽  
Eni Kusrini ◽  
Erma P. Hayuningtiyas ◽  
Shofihar Sinansari ◽  
Rudhy Gustiano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Gene Sequence ◽  
Ornamental Fish ◽  
Coi Gene ◽  
Tree Construction ◽  
In The Wild ◽  
Blast Program

The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

scholarly journals DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Ninis trisyani Margono ◽  
DWI ANGGOROWATI RAHAYU
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Wide Distribution ◽  
Coi Gene ◽  
Razor Clam ◽  
Molecular Phylogenetic ◽  
Solen Grandis

Abstract. Trisyani N, Rahayu DA. 2020. DNA barcoding of razor clam Solen spp. (Solinidae, Bivalva) in Indonesian beaches. Biodiversitas 21: 478-484. Solen spp. are shells with various morphological characteristics with a wide distribution of tropical and subtropical beaches, including Indonesia. The identification of Solen spp. is generally based on its morphological characteristics. This method is very problematic due to specimens share similarity in morphology and color. This study was using DNA barcode as a molecular identification tool. The bivalve COI sequence was amplified using PCR and molecular phylogenetic analysis using the Neighbor-Joining method. The amplified COI gene has a length of about 665 bp. The purpose of this study was to evaluate genetic variation and compare the phylogenetic Solen spp. in Indonesian waters. The composition of the nucleotide bases of Solen spp. the comparative species are A = 26.79%, C = 23.16%, G = 19.17% and T = 30.93%. The total nucleotide base A + T was 57.72%, while G + C was 42.33%. The results of phylogenetic analysis showed that Solen spp. Cirebon and Jambi are in one clade with Solen regularis with genetic distance 0.000 - 0.002. Solen spp. Surabaya, Bangkalan, Pamekasan, and Sumenep are in separate clades and are related to Solen grandis, Solen stricus and Solen lamarckii with genetic distance from 0.146 - 0.156. The diversity of nucleotide was 0.9780 and was divided into 12 haplotypes.

DNA barcoding unravels three new species and a subspecies of Olepa Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes

2020 ◽  
Vol 19 (2) ◽  
pp. 44-60
Author(s):  
APARNA SURESHCHANDRA KALAWATE ◽  
K. P. DINESH ◽  
A. SHABNAM
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Coi Gene ◽  
Male And Female ◽  
Morphological Variations ◽  
Three New Species ◽  
First Time ◽  
Respective Species

The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene

scholarly journals DNA barcoding of Zygaenidae (Lepidoptera): results and perspectives

2019 ◽  
Vol 42 (2) ◽  
pp. 137-150
Author(s):  
Konstantin A. Efetov ◽  
Anna V. Kirsanova ◽  
Zoya S. Lazareva ◽  
Ekaterina V. Parshkova ◽  
Gerhard M. Tarmann ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Dna Barcodes ◽  
The Family ◽  
The World ◽  
Biological Characters

The present study provides a DNA barcode library for the world Zygaenidae (Lepidoptera). This study reports 1031 sequence data of the COI gene DNA barcodes for more than 240 species in four of the five subfamilies of the family Zygaenidae. This is about 20% of the world Zygaenidae species. Our results demonstrate the specificity of the COI gene sequences at the species level in most of the studied Zygaenidae and agree with already established taxonomic opinions. The study confirms the effectiveness of DNA barcoding as a tool for determination of most Zygaenidae species. However, some of the results are contradictory. Some cases of shared barcodes have been found, as well as cases of deep intraspecific sequence divergence in species that are well separated by morphological and biological characters. These cases are discussed in detail. Overall, when combined with morphological and biochemical data, as well as biological and ecological observations, DNA barcoding results can be a useful support for taxonomic decisions.

Using DNA barcodes to detect non-indigenous species: the case of the Asian copepod Mesocyclops pehpeiensis Hu, 1943 (Cyclopidae) in two regions of the world

Crustaceana ◽  
2015 ◽  
Vol 88 (12-14) ◽  
pp. 1323-1338 ◽  
Author(s):  
Lucía Montoliu ◽  
María R. Miracle ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Exotic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Rice Paddy ◽  
Coi Gene ◽  
Individual Species ◽  
Indigenous Species ◽  
Worldwide Distribution ◽  
The World ◽  
Non Indigenous Species

To date, little attention has been paid to analyses of copepods as exotic species. The genusMesocyclops, a freshwater cyclopoid, has a worldwide distribution, but individual species within the genus have a quite restricted geographical range.Mesocyclops pehpeiensisHu, 1943 is a Central-East Asian species, rarely found outside of this area, and when it appears should be considered as non-native. Based on morphology and DNA barcode analyses, using the COI gene, we confirmed records ofM. pehpeiensisin two ponds in Mexico and in a rice paddy near Valencia, Spain. The morphology of this species, based on morphometric analyses, was found to be variable, but DNA barcoding confirmed the same identity for specimens from two continents. The extremely low COI genetic divergence among these disjunct populations ofM. pehpeiensisstrongly evidences anthropogenic translocations. DNA barcoding can be a fast and useful analytical tool to accurately identify exotic species across the world.

scholarly journals Phylogenetic relationships of stress resistant fish in Harapan Rainforest Jambi based on DNA barcode

2021 ◽  
Vol 21 (2) ◽  
pp. 75-87
Author(s):  
Tedjo Sukmono ◽  
Winda Dwi Kartika
Keyword(s):  
Genetic Distance ◽  
Dna Extraction ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Dna Barcode ◽  
Gene Bank ◽  
Coi Gene ◽  
Rad Sequencing ◽  
Study Centre ◽  
Channa Striata

DNA barcode as an effective tool for identification and reveal phylogenetic relationships in fish. The purpose of this study was to analysis DNA sequence, genetic distance and reveal phylogenetic relationships of stress resistance fish (blackfish) in Harapan Rainforest Jambi base on DNA barcode. The research was conducted from April to August 2016 in Harapan Rainforest Jambi, Integrated Laboratory, Jambi University and Biotechnology Laboratory of the Primate Study Centre-IPB University. DNA extraction was done on five blackfish species from Harapan Rainforest Jambi, namely Nandus nebulosus, Pristolepis grootii, Trichopodus leerii, Channa striata and Channa micropeltes. As a comparison, we used stress intolerance fish (whitefish) from Harapan Rainforest Jambi, i.e., Balantiocheilos melanopterus and Hemibagrus nemurus from the gene-bank NCBI with acession number KT001040,1. DNA Extraction was performed according to Quick-Star Tissue Protocol from Qiagen. COI gene amplification with modification at denaturation and anneling temperatures. Visualization DNA band using a horizontal electrophoresis machine from Bio Rad. Sequencing DNA send to 1st Base Malaysia. DNA sequence used Biodit and MEGA X software. The alignment of the DNA bands in MEGA X produces DNA sequence along 588 bp, where 350 bp conserve and 238 bp variable sites. The composition of the base nucleotides were (T/U) =29%, C=28.6%, A=25%, and G=17.3%. The closest genetic distance was between Channa striata and Channa micropeltes (0.190)  and the farthest was found on  Nandus nebulosus and  Hemibagrus nemurus (0.303). The phylogeny tree shows that the blackfishes are separated from whitefishes. The group of blackfish is divided into Channidae group (Channa striata, Channa micropeltes) and non-Channidae group (Nandus nebulosus, Trichopodus leerii, Pristolepis grootii).

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

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